ArticleNucleic acids research2013
Automated and assisted RNA resonance assignment using NMR chemical shift statistics.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- NMR structures of small molecules bound to a model of a CUG RNA repeat expansion.Bioorganic & medicinal chemistry letters · 2024Review
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- NMR structures of small molecules bound to a model of an RNA CUG repeat expansion.bioRxiv : the preprint server for biology · 2024Article
- Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility.Nature communications · 2023Article
- Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor.Nature communications · 2023Article
- Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA.Frontiers in molecular biosciences · 2023Article
- A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript.Nucleic acids research · 2022Article
- Article
- Bayesian probabilistic assignment of chemical shifts in organic solids.Science advances · 2021Article
- Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment.Molecules (Basel, Switzerland) · 2021Article
- Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states.Nature communications · 2021Article
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
- Automatic structure-based NMR methyl resonance assignment in large proteins.Nature communications · 2019Article
- An unexpected RNA distal interaction mode found in an essential region of the hepatitis C virus genome.Nucleic acids research · 2018Article
- Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.Journal of biomolecular NMR · 2018Article
- Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach.Chemistry (Weinheim an der Bergstrasse, Germany) · 2018Article
- Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment.Nucleic acids research · 2017Article
- Integrative NMR for biomolecular research.Journal of biomolecular NMR · 2016Article
- High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone.Journal of biomolecular NMR · 2015Article
- Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.Journal of biomolecular NMR · 2015Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and (1)H and (13)C chemical shifts. Statistics of resonances from regularly Watson-Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1'/C1' chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92-100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding (13)C resonances, which provides an important step toward automated structure determination of RNAs.
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